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新型コロナウイルスの構造情報

このページの他言語版もあります: English简体中文繁體中文한국어
コロナウイルス
コロナウイルス, 2020. David S. Goodsell@RCSB PDB による原画を修正

最近、新型コロナウイルス感染症（Novel Coronavirus disease 2019: COVID-19）の拡大が世界中で深刻な問題となっています。早急にこの新型ウイルス（Severe Acute Respiratory Syndrome Coronavirus 2: SARS-CoV-2）を理解し有効な薬を開発するため，関連するタンパク質の構造研究は既に始まっています。そして，解明された構造はPDBに登録されていっています。PDBjでは利用者の利便を図るため，新型コロナウイルス特集ページを作成しました。新たなエントリーが毎週水曜日の週次更新で公開されると、同時にこのページにも追加されます。

またこのウイルスのタンパク質に関する解説記事を以下の「今月の分子」ページに掲載しています。

「全エントリー」のタブでは，同じ著者によるグループ登録のエントリーも全て区別し，すべてのPDB IDを省略せず表示しています。 「代表構造」タブには最も分解能の高い代表構造のみを表示しており，アミノ酸配列が100%同じPDBエントリーはリガンドが異なるものも含め除外してあります。 「最新のエントリー」のタブは，今週公開された最も新しいエントリーです。

作成日: 2020-09-03 (最終更新日: more than 1 year ago)2022-09-02
全エントリー (4559)代表構造 (2032)最新のエントリー (12)
9FEH
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BU of 9feh by Molmil
Crystal structure of SARS-CoV-2 nsp14 methyltransferase domain in complex with the STM957 inhibitor
分子名称: Transcription factor ETV6,Guanine-N7 methyltransferase nsp14, ZINC ION, ~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-(2-pyridin-3-ylethynyl)pyrrolo[2,3-d]pyrimidin-7-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl]-3-cyano-~{N}-ethyl-4-methoxy-benzenesulfonamide
著者Zilecka, E, Klima, M, Boura, E.
登録日2024-05-20
公開日2024-08-28
最終更新日2024-09-04
実験手法X-RAY DIFFRACTION (1.99 Å)
主引用文献Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39.
J Struct Biol X, 10, 2024
8KEH
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BU of 8keh by Molmil
State 2 of SARS-CoV-2 XBB Variant Spike protein trimer complexed with antibody PW5-5
分子名称: PW5-5 heavy chain, PW5-5 light chain, Spike glycoprotein
著者Sun, L, Mao, Q, Wang, Y.
登録日2023-08-11
公開日2024-09-04
実験手法ELECTRON MICROSCOPY (3.21 Å)
主引用文献Potent and broadly neutralizing antibodies against sarbecoviruses induced by sequential COVID-19 vaccination.
Cell Discov, 10, 2024
8Y4C
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BU of 8y4c by Molmil
BA.2.86 S-trimer in complex with Nab XGv280
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, XGv280 Heavy chain, ...
著者Zhu, Q, Liu, P.
登録日2024-01-30
公開日2024-09-04
実験手法ELECTRON MICROSCOPY (3.75 Å)
主引用文献Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope.
Signal Transduct Target Ther, 9, 2024
8ZER
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BU of 8zer by Molmil
Crystal structure of the complex of Wuhan SARS-CoV-2 RBD (319-541) with P2C5 nanobody
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody P2C5, Spike protein S1, ...
著者Sluchanko, N.N, Varfolomeeva, L.A, Shcheblyakov, D.V, Logunov, D.Y, Gintsburg, A.L, Popov, V.O, Boyko, K.M.
登録日2024-05-06
公開日2024-09-04
最終更新日2024-09-18
実験手法X-RAY DIFFRACTION (3.1 Å)
主引用文献Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain.
Biochemistry Mosc., 89, 2024
8ZES
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BU of 8zes by Molmil
Crystal structure of the Wuhan SARS-CoV-2 RBD (333-541) complexed with P2C5 nanobody
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanobody P2C5, ...
著者Sluchanko, N.N, Varfolomeeva, L.A, Shcheblyakov, D.V, Logunov, D.Y, Gintsburg, A.L, Popov, V.O, Boyko, K.M.
登録日2024-05-06
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (3.7 Å)
主引用文献Structural Basis for Evasion of New SARS-CoV-2 Variants from the Potent Virus-Neutralizing Nanobody Targeting the S-Protein Receptor-Binding Domain.
Biochemistry Mosc., 89, 2024
9EO6
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BU of 9eo6 by Molmil
SARS-CoV2 major protease in complex with a covalent inhibitor SLL11.
分子名称: 3C-like proteinase nsp5, Inhibitor SLL11, POTASSIUM ION
著者Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
登録日2024-03-14
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.11 Å)
主引用文献Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 68, 2024
9EOR
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BU of 9eor by Molmil
SARS-CoV2 major protease in complex with a covalent inhibitor SLL12.
分子名称: 3C-like proteinase nsp5, Inhibitor SLL12, POTASSIUM ION
著者Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
登録日2024-03-15
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.25 Å)
主引用文献Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 68, 2024
9EOX
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BU of 9eox by Molmil
SARS-CoV2 major protease in covalent complex with a soluble inhibitor.
分子名称: 3C-like proteinase nsp5, POTASSIUM ION, Soluble inhibitor
著者Moche, M, Lennerstrand, J, Nyman, T, Strandback, E, Akaberi, D.
登録日2024-03-15
公開日2024-09-04
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (2.54 Å)
主引用文献Identification of novel and potent inhibitors of SARS-CoV-2 main protease from DNA-encoded chemical libraries.
Antimicrob.Agents Chemother., 68, 2024
8Y4A
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BU of 8y4a by Molmil
BA.2.86 S-trimer in complex with Nab XG2v046
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein, ...
著者Zhu, Q, Liu, P.
登録日2024-01-30
公開日2024-09-11
最終更新日2024-10-09
実験手法ELECTRON MICROSCOPY (3.4 Å)
主引用文献Enhancing RBD exposure and S1 shedding by an extremely conserved SARS-CoV-2 NTD epitope.
Signal Transduct Target Ther, 9, 2024
8U3O
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BU of 8u3o by Molmil
SARS-CoV-2 Main Protease A173V in complex with CDD-1819
分子名称: (2P)-2-(isoquinolin-4-yl)-1-[(1s,3R)-3-(methylcarbamoyl)cyclobutyl]-N-[(1S)-1-(naphthalen-2-yl)ethyl]-1H-benzimidazole-7-carboxamide, ORF1a polyprotein
著者Nnabuife, C, Palzkill, T.
登録日2023-09-08
公開日2024-09-18
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献SARS-CoV-2 Main Protease A173V in complex with CDD-1819
To Be Published
8ZBQ
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BU of 8zbq by Molmil
Local map of Omicron Subvariant JN.1 RBD with ACE2
分子名称: Angiotensin-converting enzyme 2, Spike protein S2'
著者Yan, R.H, Yang, H.N.
登録日2024-04-27
公開日2024-09-18
最終更新日2024-09-25
実験手法ELECTRON MICROSCOPY (3.03 Å)
主引用文献Structural basis for the evolution and antibody evasion of SARS-CoV-2 BA.2.86 and JN.1 subvariants.
Nat Commun, 15, 2024
9ATO
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BU of 9ato by Molmil
XBB.1.5 spike/Nanosota-3C complex
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Nanosota-3C, ...
著者Ye, G, Bu, F, Liu, B, Li, F.
登録日2024-02-27
公開日2024-09-18
最終更新日2024-10-16
実験手法ELECTRON MICROSCOPY (3.2 Å)
主引用文献Structure of XBB.1.5 spike/Nanosota-3C complex
To Be Published
8WFH
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BU of 8wfh by Molmil
Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
分子名称: D1 scFv, Spike protein S1
著者Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
登録日2023-09-19
公開日2024-09-25
実験手法X-RAY DIFFRACTION (2.72 Å)
主引用文献Crystal structure of Omicron BA.4/5 in complex with a neutralizing antibody scFv D1
To Be Published
8WFM
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BU of 8wfm by Molmil
Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
分子名称: Spike protein S1, T11 scFv
著者Zhang, M, Zhang, N, Gabibov, A, Guo, Y.
登録日2023-09-19
公開日2024-09-25
最終更新日2024-10-09
実験手法X-RAY DIFFRACTION (2.99 Å)
主引用文献Crystal structure of Omicron BA.1 in complex with a neutralizing antibody scFv T11
To Be Published
9DN4
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BU of 9dn4 by Molmil
Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N
分子名称: CHLORIDE ION, FAB BL3-6S97N HEAVY CHAIN, FAB BL3-6S97N LIGHT CHAIN, ...
著者Lovell, S, Cooper, A, Battaile, K.P, Hegde, S, Wang, J.
登録日2024-09-16
公開日2024-09-25
最終更新日2024-10-16
実験手法X-RAY DIFFRACTION (1.9 Å)
主引用文献Crystal structure of a SARS-CoV-2 20-mer RNA in complex with FAB BL3-6S97N
To be published
8WKE
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BU of 8wke by Molmil
Sulfate-bound SARS-CoV-2 Nsp9
分子名称: Non-structural protein 9, SULFATE ION
著者Chen, P.J, Huang, H.Y, Hsiao, W.C, Huang, C.Y.
登録日2023-09-27
公開日2024-10-02
実験手法X-RAY DIFFRACTION (2.12 Å)
主引用文献Sulfate-bound SARS-CoV-2 Nsp9
To Be Published
8WSJ
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BU of 8wsj by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=6.5
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.74 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=6.5
To Be Published
8WSK
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BU of 8wsk by Molmil
Crystal structure of SARS-Cov-2 main protease, pH=8.5
分子名称: 3C-like proteinase nsp5
著者Jiang, H.H, Zhou, X.L, Zhang, J, Li, J.
登録日2023-10-17
公開日2024-10-02
実験手法X-RAY DIFFRACTION (1.88 Å)
主引用文献Crystal structure of SARS-Cov-2 main protease, pH=8.5
To Be Published
8K18
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BU of 8k18 by Molmil
Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
分子名称: Spike protein S1, ZCP4C9 heavy chain, ZCP4C9 light chain
著者Bingjie, T, Shangyu, D.
登録日2023-07-10
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (3.68 Å)
主引用文献Neutralization antibody ZCP4C9 bound with SARS-CoV-2 Omicron BA.5 RBD
To Be Published
8K19
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BU of 8k19 by Molmil
Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
分子名称: Spike protein S1, ZCP3B4 heavy chain, ZCP3B4 light chain
著者Tang, B, Dang, S.
登録日2023-07-10
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (3.88 Å)
主引用文献Neutralization antibody ZCP3B4 bound with SARS-CoV-2 Omicron BA.5 RBD
To Be Published
8WXL
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BU of 8wxl by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike glycoprotein (closed state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2023-10-30
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (2.59 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Nat Commun, 2024
8XUX
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BU of 8xux by Molmil
Structure of the SARS-CoV-2 BA.2.86 spike protein (1-up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Spike glycoprotein
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (3.22 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Nat Commun, 2024
8XV0
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BU of 8xv0 by Molmil
Structure of SARS-CoV-2 BA.2.86 spike RBD in complex with ACE2 (up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-14
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (3 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Nat Commun, 2024
8XVM
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BU of 8xvm by Molmil
Structure of SARS-CoV-2 BA.2.86 spike glycoprotein in complex with ACE2 (3-up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-01-15
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (2.77 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Nat Commun, 2024
9IU1
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BU of 9iu1 by Molmil
Structure of SARS-CoV-2 JN.1 spike RBD in complex with ACE2 (up state)
分子名称: 2-acetamido-2-deoxy-beta-D-glucopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, Processed angiotensin-converting enzyme 2, ...
著者Yajima, H, Anraku, Y, Kita, S, Kimura, K, Maenaka, K, Hashiguchi, T.
登録日2024-07-20
公開日2024-10-09
実験手法ELECTRON MICROSCOPY (4.3 Å)
主引用文献Structural basis for receptor-binding domain mobility of the spike in SARS-CoV-2 BA.2.86 and JN.1
Nat Commun, 2024

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件を2024-10-16に公開中

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